NOTE: the LB amount is WRONG on the handout - they should only make 100ml of LB.
When they work in pairs - have them start out on the 'expensive' stuff first. That way if they have to finish the lab another day and end up both doing the materials separately - we won't have made too much stuff.
'Expensive' stuff:
0.100 L LB broth (autoclaved) 200 ml 0.1M Tris base or Trizma base pH 7.5 using conc. HCl (hydrochloric acid) 1 ml 50 mg/ml Amp (filter sterilized) 50 ml 1 M Imidazole (filter-sterilized) 50 ml 10x PBS (Phosphate Buffered Saline, filter-sterilized)
'Cheap' stuff:
50 ml 5 N NaOH (Sodium Hydroxide) 100 ml 5x Tris-Glycine-SDS buffer 10 ml of 30% EtOH (ethanol) in autoclaved water
PyMOL1
Common Comments - Pymol1
Improve pics, no 'stretched' images
Improve captions
Analysis is not analysis, too many instructions or personal reflections
Label All atoms
Missing labels
Missing distance labels
Don't use white out, just cross out
Caption below figures and above tables
Do not write 'this image shows'...
Tips & Hints
Lab Safety - no liquids in lab to prevent electrocution
Materials - computer, PyMol program, helix.pdb, Betasheet.pdb
Figure captions - should include "carbons as green, oxygens as red, nitrogens as blue ....... etc. "
Show them how to do CROP in Word - to resize images.
When measuring across the helix for the diameter, they won't be able to go directly across the width (it will be on an angle).
They should be sure to address this in their comments and/or error analysis.
Buffer Titration
PyMol 2
Beer's Law
COMMON COMMENTS - Beer's Law
Correct images
show calculations
which spec did you use?
enough procedures but not onerous detail that is redundant to lab 1
analysis-error
conclusion-recap
future directions
GRAPHS: 1. max wavelength 2. all readings 3. table with data 4.graph with linear regression
hypothesis: does it hold for all concentrations?
Should mention creating linear best fit line in Excel (don't need to talk about other aspects of Excel since they have already used it)
PyMol 3
Protein Expression
Virtual Screening 1
Protein Purification Lab
NOTE: each pair will pick just one (1) pellet to purify. The other one should just be kept frozen as backup.
- each person should still make their own samples 1,2,3,4,5,6 for the Gel Though
Also, if they use Cyanase - they only need 1 ul of it since the stock concentration is greater than that of benzonase.
Teaching Points For VDS Spring 2014 Labs
General Tips & Hints
show them how to use UTBox.
http://www.utexas.edu/its/cloudstorage/
Timestamp for Microsoft Word documents: ALT + i together, release and hit T
Date Stamp for Excel: CTRL + ;
Time Stamp for Excel: CTRL + SHFT + :
For each week, see folder in VDS Staff Google Docs account for teaching points
some are password protected with Mentor password
https://drive.google.com/folderview?id=0B_Gl3lMyhDsoUkZhaG16UjA5b3c&usp=sharing
NOTES ABOUT EACH LAB:
Lit Search & Endnote Web
Buffers & Solutions Lab:
NOTE: the LB amount is WRONG on the handout - they should only make 100ml of LB.When they work in pairs - have them start out on the 'expensive' stuff first. That way if they have to finish the lab another day and end up both doing the materials separately - we won't have made too much stuff.
'Expensive' stuff:
0.100 L LB broth (autoclaved)200 ml 0.1M Tris base or Trizma base pH 7.5 using conc. HCl (hydrochloric acid)
1 ml 50 mg/ml Amp (filter sterilized)
50 ml 1 M Imidazole (filter-sterilized)
50 ml 10x PBS (Phosphate Buffered Saline, filter-sterilized)
'Cheap' stuff:
50 ml 5 N NaOH (Sodium Hydroxide)100 ml 5x Tris-Glycine-SDS buffer
10 ml of 30% EtOH (ethanol) in autoclaved water
PyMOL1
Common Comments - Pymol1Improve pics, no 'stretched' images
Improve captions
Analysis is not analysis, too many instructions or personal reflections
Label All atoms
Missing labels
Missing distance labels
Don't use white out, just cross out
Caption below figures and above tables
Do not write 'this image shows'...
Tips & Hints
Lab Safety - no liquids in lab to prevent electrocution
Materials - computer, PyMol program, helix.pdb, Betasheet.pdb
Figure captions - should include "carbons as green, oxygens as red, nitrogens as blue ....... etc. "
Show them how to do CROP in Word - to resize images.
When measuring across the helix for the diameter, they won't be able to go directly across the width (it will be on an angle).
They should be sure to address this in their comments and/or error analysis.
Buffer Titration
PyMol 2
Beer's Law
COMMON COMMENTS - Beer's Law
Correct images
show calculations
which spec did you use?
enough procedures but not onerous detail that is redundant to lab 1
analysis-error
conclusion-recap
future directions
GRAPHS: 1. max wavelength 2. all readings 3. table with data 4.graph with linear regression
hypothesis: does it hold for all concentrations?
Should mention creating linear best fit line in Excel (don't need to talk about other aspects of Excel since they have already used it)
PyMol 3
Protein Expression
Virtual Screening 1
Protein Purification Lab
NOTE: each pair will pick just one (1) pellet to purify. The other one should just be kept frozen as backup.- each person should still make their own samples 1,2,3,4,5,6 for the Gel Though
Also, if they use Cyanase - they only need 1 ul of it since the stock concentration is greater than that of benzonase.
Virtual Screening 2
Protein Characterization Lab
VS3 lab
Target Discovery
Enzyme Assay Lab